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Changes
Tried a different link formatting for the trackers - by including the full name.
* The relax_disp.plot_disp_curves user function can now support 150 sets per Grace graph.
* The relax_disp.plot_disp_curves user function can now support 3000 sets per Grace graph.
* System test for sequence read expanded to include assertions of correct data. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Added some more files for the Fyn SH3 R<sub>1ρ</sub> test data. This includes the cpmg_fit input and output files, R<sub>1</sub> data files for relax as R<sub>1</sub> cannot optimised yet, and a relax script.
* Added system test for reading spins from a Sparky list. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added interpreter.spectrum.read_spins function. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Created the back end function for the read_spins function. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Fix for system test. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Extended reading of Sparky files to include residue names. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Expanded system test and made it pass for user function spectrum.read_spins. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Updated the GUI test to check for first ID in list. Fix for [https://gna.org/bugs/?21076 bug #21076] - When loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur.
* Added keyword dim to frontend function for spectrum.read_spins(). Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list]. This is associate data with the spins of up to two dimensions.* Implemented system test for reading spins from NMRPipe SeriesTab formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Extended reading of spin residue names from NMRPipe SeriesTab formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Modified NMRPipe SeriesTab to read residue numbers and name for two-dimensional list. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Insert check if spin already exist before creating it. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Issuing a warning instead of error when loading spins from Sparky list where residue names are not present. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Issued a warning instead of error when loading spin residue names from a NMRPipe SeriesTab formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Changed to use return_spin for testing presence of spin. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Implemented another system test for reading NMRPipe SeriesTab files. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Fix for issuing a warning in reading spins from a NMRPipe SeriesTab formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Fix for issuing a warning when reading spins from a Sparky formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Implemented system test for reading spin IDs from NMRView formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Made reading of NMRView formatted file return the residue number as integer instead of string. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Fix for calling the warn() function. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Extended the error description for reading NMRView files. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Implemented system test for reading spins from a NMRPipe SeriesTab formatted file whereby the assignments for second dimension is missing. This will be a typically export from Sparky, converted to NMRPipe format, and processed with SeriesTab. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Fixed for reading spins from a NMRPipe SeriesTab formatted file whereby dimension 2 misses residue number and residue name. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Expanded the warning message for a system test. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Modified system test for reading an assignment whereby the second dimension is missing. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* If dimension 2 in a SeriesTab formatted file does not contain residue number+name, it defaults to the dimension 1. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Implemented system test for reading spins from an XEasy file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Modified XEasy reading function to pass residue names back. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Copied a SeriesTab file for the implementation of double assignments in Sparky files.
* Redesign of the CPMG frequency and spin-lock field strength data structures. These now have an extra dimension for the offset so that the values are now experiment, magnetic field strength and offset dependent. If many offsets are present but are variable for each dispersion point, then this saves a lot of calculation time. This mainly affects R<sub>1ρ</sub>-type data. To better handle this, all of the specific_analyses.relax_disp.disp_data.loop_*() functions have been modified to accept data values rather than indices.
* Improved the printout of the relax_disp.r2eff_read_spin user function for the R<sub>2eff</sub> keys.
* Extended the system test for reading spins from Sparky files with empty residue name+number second dimension assignment. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Modified the Sparky peak list for two dimensional assignment example. This will typically be the export from CcpNmr Analysis. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Implemented a system test for using double assignments in Sparky formatted files. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Extended reading of spins from Sparky files for up to two dimensional assignments. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added example of CcpNmr analysis exported Sparky file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added system test for reading CcpNmr Analysis exported Sparky file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Modified the reading of Sparky files when exported from CcpNmr Analysis. The keyword 'Data' is not present here. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added a system test for using generic file for reading spins. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Modified the generic list to also return spin information when intensity is not present. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added another system test for returning spins from a generic file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Added residue 4 to the R<sub>2eff</sub> files for the truncated CPMG data from Flemming Hansen.
* Added cpmg_fit results to the software comparison table for Flemming Hansen's CPMG data. The cpmg_fit input and log files have been added as well.
* Shifted the software comparison down a directory so it can be used for all the different data.
* Added system test for reading chemical shift from NMRPipe SeriesTab file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Implemented reading of chemical shifts from NMRPipe SeriesTab formatted files. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Additional chemical shift reading test for SeriesTab formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Improvements for the find_intensity_keys() dispersion analysis function. This now handles the reference point None being converted to NaN in numpy arrays and the logic is now clearer.
* Changed some warnings in the dispersion analysis so they only show if R<sub>1ρ</sub> data is loaded. This is for missing chemical shifts and R<sub>1</sub> data.
* Added support for the [[NS R1rho 3-site]] models to the relax_disp.select_model user function back end. This is for the [[NS R1rho 3-site]] and [[NS R1rho 3-site linear]] CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.
* Decreased the amount of synthetic data in the ns_r1rho_3site_linear test suite shared data directory. The number of offsets for this [[NS R1rho 3-site linear]] model synthetic data has been decreased from 81 points to 21. This is because the large quantities of data slow the test suite down too much.
* Added a GUI test for reading spins from a spectrum formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added the GUI key 'new spectrum' to point to 'spectrum.read_spins'. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added the spectrum.read_spins GUI page for reading spins from a spectrum formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Added radio button for reading spins from a spectrum formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].* Further added to the GUI test for reading spins from spectrum formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Speed up of the Relax_disp.test_ns_r1rho_3site_linear system test. Half of the data has been commented out, as too much data was being loaded for the test.
* Created the target functions for the [[NS R1rho 3-site]] models. This is for the [[NS R1rho 3-site]] and [[NS R1rho 3-site linear]] dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
* Added the R<sub>2eff</sub> calculating functions for the [[NS R1rho 3-site]] models to the relax library. This is for the [[NS R1rho 3-site]] and [[NS R1rho 3-site linear]] dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
* Fix for GUI text string for the select radio button for reading spins from a spectrum formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Bug fix for the new [[NS R1rho 3-site]] dispersion models - the Y and Z initial magnetisations were switched. This is for the [[NS R1rho 3-site]] and [[NS R1rho 3-site linear]] dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
* Added cpmg_fit results for the program modified to turn off the PEAK_SHIFT flag. These are the results which should most closely match the relax results. This is for the simulated R<sub>1ρ</sub> data for the [[NS R1rho 3-site linear]] model.
* Updated the relax results for the Fyn SH3 R<sub>1ρ</sub> dispersion data. This is for the recent changes to the [[NS R1rho 2-site]] dispersion model.
* Updated the Relax_disp.test_ns_r1rho_3site_linear system test so it now passes. The chi-squared value is not exactly zero as there are numerical differences between relax and cpmg_fit due to different approaches being used.
* Added the RMSD determined via showApod for the 69 experiments. Work in progress for [https://gna.org/support/?3083 Support Request #3083] - Addition of Data-set for R<sub>1ρ</sub> analysis].* Added system test for the analysis of optimisation of the Kjaergaard et al., 2013 Off-resonance R<sub>1ρ</sub> relaxation dispersion experiments using the [[DPL94|DPL]] model. Work in progress for [https://gna.org/support/?3083 Support Request #3083] - Addition of Data-set for R<sub>1ρ</sub> analysis].* Modified analysis script for example data of R<sub>1ρ</sub>. Work in progress for [https://gna.org/support/?3083 Support Request #3083] - Addition of Data-set for R<sub>1ρ</sub> analysis].
* Created synthetic R<sub>1ρ</sub> dispersion data for the [[NS R1rho 3-site]] model. This is a simple modification of the data for the [[NS R1rho 3-site linear]] model. The k_AC parameter was simply changed from 0 to 1000. The cpmg_fit software was used to create the data. Both cpmg_fit and relax results have been updated to the new model.
* Created the new Relax_disp.test_ns_r1rho_3site system test. This was copied from the Relax_disp.test_ns_r1rho_3site_linear test and modified to use the new [[NS R1rho 3-site]] model synthetic data.
* Fix for wrong use of relax_fit.relax_time instead of relax_disp.relax_time. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Added the ns_r1rho_3site module to the lib.dispersion package __all__ list. This allows the unit tests to pass.
* turned off a system test until the release of relax 3.1.1 is over. Work in progress for [https://gna.org/support/?3044 Support Request #3044] - load spins from Sparky list].
* Fix for the Relax_disp.test_bug_21076_multi_col_peak_list GUI test. The peak intensity wizard is now closed at the end of the test so that subsequent tests can cleanly operate. Without closing this wizard, launching it a second time in another test will always fail.
* Capitalised 'Python' in the IO redirection messages.
* Basic fix for the Relax_disp.test_r2eff_read_spin system test - the CPMG frequencies are now set. This was identified in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774.
* Fixes for the parameters in the Relax_disp.test_ns_mmq_3site system test script.
* Fix for optimisation of Dr. Flemming Hansen's CPMG data to the [[NS CPMG 2-site star]] dispersion model. Fix for [https://gna.org/bugs/?21322 bug #21322] - 5x Test suite fail for version 3.1.0, reported for system CentOS 2.6.32-358.18.1.el6.x86_64]. Adjusted p<sub>A</sub>, Δω, k<sub>ex</sub>, χ<sup>2</sup>.* Fix for optimisation of the Korzhnev et al., 2005 <sup>15</sup>N DQ CPMG data using the [[MMQ 2-site]] model. Fix for [https://gna.org/bugs/?21322 bug #21322] - 5x Test suite fail for version 3.1.0, reported for system CentOS 2.6.32-358.18.1.el6.x86_64].* Fix for optimisation of the Korzhnev et al., 2005 <sup>15</sup>N MQ CPMG data using the [[MMQ 2-site]] model. Fix for [https://gna.org/bugs/?21322 bug #21322] - 5x Test suite fail for version 3.1.0, Reported reported for system CentOS 2.6.32-358.18.1.el6.x86_64].* Fix for optimisation of the Korzhnev et al., 2005 <sup>15</sup>N ZQ CPMG data using the [[MMQ 2-site]] model. Fix for [https://gna.org/bugs/?21322 bug #21322] - 5x Test suite fail for version 3.1.0, Reported reported for system CentOS 2.6.32-358.18.1.el6.x86_64].* Fix for optimisation of all the Korzhnev et al., 2005 CPMG data using the [[MMQ 2-site]] model. Fix for [https://gna.org/bugs/?21322 bug #21322] - 5x Test suite fail for version 3.1.0, Reported reported for system CentOS 2.6.32-358.18.1.el6.x86_64].* Fix for optimisation of Dr. Flemming Hansen's CPMG data to the [[NS CPMG 2-site star]] dispersion model. Changed so assertAlmostEqual matches 2 digits. Fix for [https://gna.org/bugs/?21322 bug #21322] - 5x Test suite fail for version 3.1.0, reported for system CentOS 2.6.32-358.18.1.el6.x86_64].
* Bug fixes for the dispersion analysis when certain data sets are completely missing.
* Fix for loading a seriesTab formatted intensity, and getting the ID for the following GUI elements. Fix for [https://gna.org/bugs/?21076 bug #21076] - when loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur.